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- PDB-5kjr: Crystal structure of the ADCC-potent antibody N60-i3 Fab in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5kjr | ||||||
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Title | Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1. | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tolbert, W.D. / Pazgier, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability. Authors: Ding, S. / Tolbert, W.D. / Prevost, J. / Pacheco, B. / Coutu, M. / Debbeche, O. / Xiang, S.H. / Pazgier, M. / Finzi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 315.9 KB | Display | ![]() |
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PDB format | ![]() | 254.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4rfoS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24412.373 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3 Cell line (production host): HEK 293 CELLS / Production host: ![]() ![]() |
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#4: Antibody | Mass: 23342.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3 Cell line (production host): HEK 293 CELLS / Production host: ![]() ![]() |
-Protein / Protein/peptide / Sugars , 3 types, 12 molecules GN![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 39144.367 Da / Num. of mol.: 1 / Mutation: W69A, S115W, H375S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | |
#5: Sugar | ChemComp-NAG / ![]() |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/MPD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-MPD / (![]() |
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#7: Water | ChemComp-HOH / ![]() |
-Details
Compound details | THE CD4-MIMETIC MINIPROTEINS INHIBIT HIV-1 ENTRY AND ARE DERIVED FROM SCYLLATOXIN (A SCORPION TOXIN) ...THE CD4-MIMETIC MINIPROTEI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.06 % |
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Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 10-16% PEG 8000, 0.1 M TRIS-HCL PH 8.5, 65 MM NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2016 / Details: RH Coated Flat mirror |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.98→50 Å / Num. obs: 19540 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.98→3.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 1.2 / % possible all: 67.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4RFO Resolution: 2.98→50 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.807 / SU B: 72.387 / SU ML: 0.586 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.562 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.54 Å2
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Refinement step | Cycle: 1 / Resolution: 2.98→50 Å
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Refine LS restraints |
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